Fig. 4: Gene set enrichment and cancer testis antigens.

a Bar plot of the enriched gene set (The Network of Cancer Genes) based on the gene list of all HLA class I peptides. The y-axis contains the identified gene sets that were available in the Network of Cancer Genes catalog (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1612-0). The counts on the x-axis show the number of genes that are overlapping with the identified gene sets from the catalog. The colors are used to annotate the significance of each gene set, ranging from blue to red (p-value 0.025–0.005, respectively). The p-adjusted method of Benjamini-Hochberg was used to correct for multiple comparison with a p-value cut-off of 0.05 to determine the enriched gene set. b CNET plot of enriched genes based on the same list, however, shows the top 5 enriched gene sets (indicated with a yellow dot), genes are indicated in gray and the lines represent the presence within a gene set. c Identification of established TAAs, CTAs, and medulloblastoma-associated proteins across the present immunopeptidome dataset. (Left column) HLA class I peptides derived from 116 naturally presented TAAs and CTAs were identified, and 16 were represented by medulloblastoma-associated peptides on at least two tumors (highlighted with orange diamonds). The frequency of positive immunopeptidomes was assessed based on HLA class I peptides for tumor samples, whereby benign hits were reported independent of HLA binding probabilities of the underlying peptide identifications. (Right column) HLA class II peptides derived from 85 naturally presented TAAs and CTAs were identified, of which eight yielded tumor-associated peptides attaining a presentation frequency of ≥7% (highlighted with orange diamonds). While peptides mapping to multiple source proteins were considered to calculate the frequency of positive immunopeptidomes, these were excluded from reporting the representation by medulloblastoma-associated peptides. CTAs and TAAs exclusively identified on benign samples were not listed. Source data are provided as a Source Data file.